Southern Sudanese show their support for secession. Photograph: Khaled El Fiqi/EPA

If south Sudan, why not south Nigeria, or north Ivory Coast, or multiple Congos? The Sudanese vote has implications for all of Africa, signalling that the borders drawn by colonial cartographers are no longer sacrosanct. Some fear it may spur the balkanisation of the continent.

"The referendum in Sudan could have a domino effect," said Shehu Sani, president of the Civil Rights Congress in Nigeria. "It is likely to be infectious to other parts of Africa in the sense that most countries , particularly in the west, are divided along the lines of Christians and Muslims."

The continent's infamously arbitrary borders – blind to ethnic, cultural and political faultlines – were drawn up by Britain and other European powers at the Berlin conference of 1884-85. When the colonies gained independence 50 years ago, the Organisation of African Unity (now the African Union) declared the borders immutable – because the alternative would look like a smashed window pane of thousands of warring states.

It is being watched closely in Nigeria, Africa's most populous country, which has its own, sometimes violent schism between a predominantly Muslim north and largely Christian, oil-rich south.

"What's happening in Sudan is raising a lot of fears, particularly in Nigeria, which is a colonial creation," said Sani. "It was thought the defeat of the Biafra [an eastern secession attempt in 1967 that led to civil war] had made division impossible, but Sudan is rekindling the thought.

"Sudan will now always be a reference point for division and secession. It will fuel the cause of people who say we cannot live together and should go our separate ways. It will encourage secessionists in Nigeria to think the same."

In recent weeks the political crisis in Ivory Coast, where President Laurent Gbagbo is resisting calls to step down, has provoked fears of renewed civil war, broadly characterised as between northern Muslims and southern Christians. Permanent separation could seem a tempting long-term solution.

But divisions in Ivory Coast are more complex than religion alone. The same is true in Sudan and Nigeria, which has more than 250 ethnic groups. Tribalism, tradition, culture and language, social and economic inequality, political marginalisation, access to resources, rural/urban rifts and the imprint of colonialism can all be manipulated by leaders to inflame tensions.

Facing so many variables, the nation-state can provide a centre of gravity. But if, as expected, south Sudan votes for independence, there are likely to be at least a few corners of Africa taking heed. Somaliland is seeking international recognition of its breakaway from Somalia, rebels in the Cabinda enclave demand separation from Angola, and Morocco has resisted proposals for a referendum on the independence of Western Sahara.

Questioning the old certainties is healthy, according to Greg Mills, head of the Brenthurst Foundation thinktank and author of Why Africa is Poor. "The fixing of borders and the absence of debate about them has protected misrule," he said. "It meant African people had little way to resist beyond armed rebellion. Sudan points the way forward for some countries, but not all."

"The 800lb gorilla in the room is Congo. [Former president] Mobutu ran it down and kept it disconnected, and various groups were marginalised. Governing Kinshasa was sufficient and he never had to extend authority to the limits of the state. Today the Congolese refuse to believe it might be better run as smaller states but, paradoxically, smaller states in Africa have been more successful."

Africa has a mosaic of young countries, though its people are as capable of patriotism as anyone when it comes to football. Fred Swaniker, founder of the African Leadership Academy, said: "I don't see the Sudan vote as a Pandora's box. While the original African borders were not necessarily drawn in a logical way, I think after 50 years most countries have accepted them and are living together.

"If anything, there's more pressure for countries to remove borders and build regional blocs to achieve economies of scale that compete with China, Brazil and India."